"Wait (for)" and "look (at)" are described as intransitive. Yet I would define them as non-idiomatic (or literal) phrasal verbs. A phrasal verb can be transitive, so why are these verbs described as intransitive???

I think, you are right, Kean. As long as these phrasal verbs aren't used idiomatically, they reveal their transitive meanings. So depending upon the preposition they can either be transitive or intransitive. For example, 'look at' I would classify as transitive, and 'look after' as intransitive. Consequently, in 'look at the boy', 'the boy' is a direct object, and in 'look after the boy', it is a prepositional one.